Minimum flows in rivers and streams aim to provide a certain level of protection for the aquatic environment. The level of protection is described by a measure such as a prescribed proportion of historic flows, wetted perimeter or suitable habitat. Conflicting minimum flow assessments from different instream flow methods are arguably the result of different environmental goals and levels of protection. The goals, the way in which levels of protection are specified, and the relationship between levels of protection and the aquatic environment are examined for three major categories of flow assessment methods: historic flow, hydraulic geometry and habitat. Basic conceptual differences are identified. Flow assessments by historic flow and hydraulic methods are related to river size and tend to retain the 'character' of a river. Habitat-based methods make no a priori assumptions about the natural state of the river and flow assessments are based primarily on water depth and velocity requirements. Flow and hydraulic methods assume that lower than natural flows will degrade the stream ecosystem, whereas habitat methods accept the possibility that aspects of the natural ecosystem can be enhanced by other than naturally occurring flows. Application of hydraulic and habitat methods suggests that the environmental response to flow is not linear; the relative change in width and habitat with flow is greater for small rivers than for large. Small rivers are more 'at risk' than large rivers and require a higher proportion of the average flow to maintain similar levels of environmental protection. Habitat methods are focused on target species or specific instream uses, and are useful where there are clear management objectives and an understanding of ecosystem requirements. Flow and hydraulic methods are useful in cases where there is a poor understanding of the ecosystem or where a high level of protection for an existing ecosystem is required.